A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2024-10-23, 21:13 CST
based on data in:
/scratch/home/dperez/resultados/VCS_p/out
General Statistics
| Sample Name | Change rate | Ts/Tv | M Variants |
|---|---|---|---|
| P1Tumor_snpEff_stats | 0 | 0.000 | 0.00M |
| P2Tumor_snpEff_stats | 0 | 0.000 | 0.00M |
SnpEff
5.2c
Annotates and predicts the effects of variants on genes (such as amino acid changes).URL: http://snpeff.sourceforge.netDOI: 10.4161/fly.19695
Variants by Genomic Region
The stacked bar plot shows locations of detected variants in the genome and the number of variants for each location.
The upstream and downstream interval size to detect these genomic regions is 5000bp by default.
Variant Effects by Impact
The stacked bar plot shows the putative impact of detected variants and the number of variants for each impact.
There are four levels of impacts predicted by SnpEff:
- High: High impact (like stop codon)
- Moderate: Middle impact (like same type of amino acid substitution)
- Low: Low impact (ie silence mutation)
- Modifier: No impact
Variants by Effect Types
The stacked bar plot shows the effect of variants at protein level and the number of variants for each effect type.
This plot shows the effect of variants with respect to the mRNA.
Variants by Functional Class
The stacked bar plot shows the effect of variants and the number of variants for each effect type.
This plot shows the effect of variants on the translation of the mRNA as protein. There are three possible cases:
- Silent: The amino acid does not change.
- Missense: The amino acid is different.
- Nonsense: The variant generates a stop codon.
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Software | Version |
|---|---|
| SnpEff | 5.2c |